Fixing upsampled spike count and alpha

apps/cadecon/src/components/controls/AlgorithmSettings.tsx

@@ -11,6 +11,8 @@ import {
   setLpFilterEnabled,
   noiseConstrained,
   setNoiseConstrained,
+  massCount,
+  setMassCount,
   maxIterations,
   setMaxIterations,
   convergenceTol,
@@ -97,6 +99,14 @@ export function AlgorithmSettings(): JSX.Element {
           onChange={setNoiseConstrained}
           disabled={isRunLocked()}
         />
+
+        <ToggleSwitch
+          label="Mass-Based Count"
+          description="Counts each event by its deconvolved mass and refits amplitude, correcting the spike overcount and halved alpha that upsampling causes (bursts closer than one kernel width may still merge)"
+          checked={massCount()}
+          onChange={setMassCount}
+          disabled={isRunLocked()}
+        />
       </div>
     </div>
   );

apps/cadecon/src/lib/algorithm-store.ts

@@ -11,6 +11,12 @@ const [lpFilterEnabled, setLpFilterEnabled] = createSignal(true);
 // still reaches the data-derived noise floor (no tuning knob). Suppresses noise
 // fit as spurious spikes; benefit concentrates at low SNR. Off = current max-PVE.
 const [noiseConstrained, setNoiseConstrained] = createSignal(true);
+// Mass-based count readout: count events by relaxed mass (calibrated to the
+// single-spike mass) and refit alpha, instead of binarize->bin-sum. Undoes the
+// coherent-grid overcount that inflates spike counts and halves alpha at high
+// upsampling. Off by default (preserves historical output); see
+// docs/cadecon-mass-count.md.
+const [massCount, setMassCount] = createSignal(false);
 // Opt-in: during each iteration, also solve every trace with the OPPOSITE
 // noise-constrained setting and store it, so the Trace Inspector can overlay the
 // two instantly (no live solve). Doubles inference cost — off by default.
@@ -63,6 +69,8 @@ export {
   setLpFilterEnabled,
   noiseConstrained,
   setNoiseConstrained,
+  massCount,
+  setMassCount,
   sparsityCompareEnabled,
   setSparsityCompareEnabled,
   maxIterations,

apps/cadecon/src/lib/bridge-effects.ts

@@ -13,6 +13,7 @@ import {
   setUpsampleTarget,
   setHpFilterEnabled,
   setLpFilterEnabled,
+  setMassCount,
   setMaxIterations,
   setConvergenceTol,
 } from './algorithm-store.ts';
@@ -47,6 +48,7 @@ function applyConfig(config: BridgeConfig): void {
   if (config.upsample_target != null) setUpsampleTarget(config.upsample_target);
   if (config.hp_filter_enabled != null) setHpFilterEnabled(config.hp_filter_enabled);
   if (config.lp_filter_enabled != null) setLpFilterEnabled(config.lp_filter_enabled);
+  if (config.mass_count != null) setMassCount(config.mass_count);
   if (config.max_iterations != null) setMaxIterations(config.max_iterations);
   if (config.convergence_tol != null) setConvergenceTol(config.convergence_tol);
   if (config.num_subsets != null) setNumSubsets(config.num_subsets);

apps/cadecon/src/lib/cadecon-pool.ts

@@ -27,6 +27,7 @@ interface TraceJobFields {
   lpEnabled: boolean;
   lambda: number;
   noiseConstrained: boolean;
+  massCount: boolean;
   computeComparison: boolean;
   warmCounts?: Float32Array;
   onComplete(result: TraceResult): void;
@@ -123,6 +124,7 @@ const caDeconRouter: MessageRouter<CaDeconPoolJob, CaDeconWorkerOutbound> = {
           lpEnabled: job.lpEnabled,
           lambda: job.lambda,
           noiseConstrained: job.noiseConstrained,
+          massCount: job.massCount,
           computeComparison: job.computeComparison,
           warmCounts: warmCopy,
         },

apps/cadecon/src/lib/iteration-manager.ts

@@ -44,6 +44,7 @@ import {
   hpFilterEnabled,
   lpFilterEnabled,
   noiseConstrained,
+  massCount,
   sparsityCompareEnabled,
   traceFistaMaxIters,
   traceFistaTol,
@@ -167,6 +168,7 @@ function dispatchTraceJobs(
   lpEnabled: boolean,
   lambda: number,
   noiseConstrained: boolean,
+  massCount: boolean,
   computeComparison: boolean,
   prevResults?: Map<number, Float32Array>,
 ): Promise<Array<Map<number, TraceResult>>> {
@@ -216,6 +218,7 @@ function dispatchTraceJobs(
         lpEnabled,
         lambda,
         noiseConstrained,
+        massCount,
         computeComparison,
         warmCounts,
         onComplete(result: TraceResult) {
@@ -454,6 +457,7 @@ export async function startRun(): Promise<void> {
   const lpOn = lpFilterEnabled();
   const sparsityLambda = 0.0;
   const noiseConstrainedOn = noiseConstrained();
+  const massCountOn = massCount();
   const computeComparison = sparsityCompareEnabled();
 
   // Create pool
@@ -592,6 +596,7 @@ export async function startRun(): Promise<void> {
       lpOn,
       sparsityLambda,
       noiseConstrainedOn,
+      massCountOn,
       computeComparison,
       prevTraceCounts,
     );
@@ -931,6 +936,7 @@ export async function startRun(): Promise<void> {
           lpEnabled: lpOn,
           lambda: sparsityLambda,
           noiseConstrained: noiseConstrainedOn,
+          massCount: massCountOn,
           computeComparison,
           warmCounts,
           onComplete(result: TraceResult) {

apps/cadecon/src/workers/cadecon-types.ts

@@ -60,6 +60,9 @@ export type CaDeconWorkerInbound =
       /** Noise-constrained threshold selection: choose the sparsest spike support
        *  whose residual meets the data-derived noise floor (no tuning knob). */
       noiseConstrained: boolean;
+      /** Mass-based count readout: count events by relaxed mass and refit alpha,
+       *  undoing the coherent-grid overcount that halves alpha (no tuning knob). */
+      massCount: boolean;
       /** Also solve with the OPPOSITE noise-constrained setting and return it as
        *  comparisonSCounts (for the teaching/impact overlay). */
       computeComparison: boolean;

apps/cadecon/src/workers/cadecon-worker.ts

@@ -38,6 +38,7 @@ function handleTraceJob(req: Extract<CaDeconWorkerInbound, { type: 'trace-job' }
       req.warmCounts ?? EMPTY_F32,
       req.lambda,
       req.noiseConstrained,
+      req.massCount,
     ) as {
       s_counts: number[];
       filtered_trace: number[] | null;
@@ -78,6 +79,7 @@ function handleTraceJob(req: Extract<CaDeconWorkerInbound, { type: 'trace-job' }
         req.warmCounts ?? EMPTY_F32,
         req.lambda,
         !req.noiseConstrained,
+        req.massCount,
       ) as { s_counts: number[] };
       comparisonSCounts = new Float32Array(cmp.s_counts);
       transfers.push(comparisonSCounts.buffer as ArrayBuffer);